Add arguments for flipping output mosaic image (#90)

README.md

@@ -26,6 +26,8 @@ optional arguments:
                         unusual microscope configurations
   --flip-y              flip tile positions top-to-bottom to account for
                         unusual microscope configurations
+  --flip-mosaic-x       flip output image horizontally
+  --flip-mosaic-y       flip output image vertically
   --output-channels [CHANNEL [CHANNEL ...]]
                         output only channels listed in CHANNELS; numbering
                         starts at 0

ashlar/reg.py

@@ -970,13 +970,15 @@ class Mosaic(object):
 
     def __init__(
             self, aligner, shape, filename_format, channels=None,
-            ffp_path=None, dfp_path=None, combined=False, tile_size=None,
-            first=False, verbose=False
+            ffp_path=None, dfp_path=None, flip_mosaic_x=False, flip_mosaic_y=False,
+            combined=False, tile_size=None, first=False, verbose=False
     ):
         self.aligner = aligner
         self.shape = tuple(shape)
         self.filename_format = filename_format
         self.channels = self._sanitize_channels(channels)
+        self.flip_mosaic_x = flip_mosaic_x
+        self.flip_mosaic_y = flip_mosaic_y
         self.combined = combined
         self.tile_size = tile_size
         self.first = first
@@ -1100,6 +1102,10 @@ def run(self, mode='write', debug=False):
                     mi_flat[p:p+w] = skimage.exposure.adjust_gamma(
                         mi_flat[p:p+w], 1/2.2
                     )
+            if self.flip_mosaic_x:
+                mosaic_image = np.fliplr(mosaic_image)
+            if self.flip_mosaic_y:
+                mosaic_image = np.flipud(mosaic_image)
             if self.verbose:
                 print()
             if mode == 'write':

ashlar/scripts/ashlar.py

@@ -41,6 +41,14 @@ def main(argv=sys.argv):
         help=('flip tile positions top-to-bottom to account for unusual'
               ' microscope configurations')
     )
+    parser.add_argument(
+        '--flip-mosaic-x', default=False, action='store_true',
+        help=('flip output image horizontally')
+    )
+    parser.add_argument(
+        '--flip-mosaic-y', default=False, action='store_true',
+        help=('flip output image vertically')
+    )
     parser.add_argument(
         '--output-channels', nargs='*', type=int, metavar='CHANNEL',
         help=('output only channels listed in CHANNELS; numbering starts at 0')
@@ -158,6 +166,8 @@ def main(argv=sys.argv):
         mosaic_args['tile_size'] = args.tile_size
     if args.quiet is False:
         mosaic_args['verbose'] = True
+    mosaic_args['flip_mosaic_x'] = args.flip_mosaic_x
+    mosaic_args['flip_mosaic_y'] = args.flip_mosaic_y
 
     try:
         if args.plates: